Protein Science C (ProtSciC)

Knowledge:

• Describe and understand details of the chemical and physical properties, reactivity and experimental analysis of amino acids, both in isolation and in the context of protein structure
• Explain and describe methods for the determination of protein structures
• Describe the basic methods and principles of NMR including its application for protein characterization

• Describe and understand basic principles in small-angle X-ray scattering
• Explain the principles of cryo-electron microscopy and X-ray crystallography and how it is applied in protein structure analysis 
• Explain the principles of single-molecule FRET and optical tweezers and how it is applied in protein science
• Understand and describe intrinsically disordered proteins in terms of biophysical properties and functional advantages
• Explain mechanism of folding and describe and apply methods for studies of protein folding and stability in vitro
• Describe and understand mechanism for protein misfolding
• Describe physical forces in terms of energy, range and dependence on geometry, environments and other parameters of importance
• Describe and understand the principle of SDS-PAGE including the stacking effect
• Describe and understand basic chromatographic theory
• Describe thermodynamically the underlying physical chemistry in protein interactions and calculate thermodynamic parameters from selected graphical presentations
• Describe and understand basic concepts in protein engineering and protein design
• Describe selected methods for high-throughput protein science

Skills:

• Integrate amino acid properties and modifications in relation to chemistry, disease and protein design
• Explain the practical matters of small-angle X-ray scattering in relation to protein structure and disorder
• Evaluate data from small-angle X-ray scattering
• Evaluate Guinier, Kratky plots and distribution functions
• Evaluate the relative advantages and disadvantages of crystallographic, cryo-EM and NMR approaches for protein structure analysis
• Evaluate qualities of experimental protein structures
• Evaluate data from single-molecule FRET including transfer efficiency histograms
• Demonstrate a thorough understanding of a selection of modern protein biophysical, spectroscopic and chemical experimental and analytical methods and assessment of when to use which method for solving a specific problem
• Understand and evaluate thermodynamics of protein folding and stability for two-state folders and understand protein folding intermediates
• Evaluate free energy landscapes and folding funnels
• Analyze phi-values in relation transition states for protein folding
• Understand how changes in protein stability can cause disease
• Describe and evaluate methods for protein quantification
• Design purification procedures based on predefined protein properties
• Evaluate and conclude on protein purity from appropriate methods
• Analyze experimental data from protein purification protocols
• Quantitatively analyze and evaluate protein-ligand and protein-protein interactions
• Understand and differentiate between agonism, antagonism and inverse agonism
• Evaluate principles of protein regulation, active site chemistry and binding
• Diagnose binding reactions qualitatively and quantitatively and analyze these
• Describe and understand the use of methods applied in protein-ligand interactions including ITC, surface plasmon resonance, fluorescence and NMR spectroscopy
• Cite and understand the use of methods applied in proteomics and functional genomics including mass spectrometry, SILAC, MS/MS, 2-D gel electrophoresis, protein and DNA arrays, fluorescence resonance energy transfer, yeast two-hybrid, pull-down assays
• Use of AlphaFold and ColabFold and assessment of reliablity and outputs
• Describe simple protein structures
• Evaluate methods and theoretical approaches to address questions in relation to protein science 
• Describe and understand the concept of hydrogen exchange in proteins
• Describe and understand interacting forces leading to higher-order protein assemblies including amyloids, fibers, condensates

Competences:

• Critically evaluate experimental results from studies of protein primary and secondary structure using protein chemistry
• Integrate and evaluate protein structure-function relationships
• Differentiate between physical forces in terms of energy, range and dependence on geometry, environments and other parameters of importance
• Critically evaluate advantages and disadvantages of different procedures used for proteins purification and characterization
• Cite, evaluate and understand various heterologous protein expression systems
• Understand and differentiate between negative and positive cooperativity in binding
• Demonstrate insight into isotope labeling, sequential assignments and evaluate the quality of NMR spectra
• Critically evaluate experimental results from single-molecule techniques including smFRET and optical tweezers
• Analyze, evaluate and condense experimental data in protein science from combinations of all possible areas of curriculum to solve relevant protein science problems
• Demonstrate oral communication in a protein scientific language
• Defining, attacking and presenting a scientific problem in protein chemistry (oral presentation)
• Communicate verbally in a scientific language and present published scientific results in power points in a clear and informative way